Roman Pavlyuchenko scored in the first half and Andrei Arshavin, coming off a two-match suspension, made it 2-0 right after the break to set up a match against the Netherlands on Saturday in Basel.
Younus recently offered to resign as captain in protest at match-fixing allegations made against him and the team by a parliamentary sports committee, even though they were cleared of any charges.
Former Pakistan captain Salim Malik was banned for life and five other players were fined in 2000 after 18 months of inquiry based on match-fixing allegations made by Latif and other Pakistan cricketers.